Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima)

Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination

(2013) Carina F Mugal et al.   BMC GENOMICS

Understanding rice domestication and implications for cultivar improvement

(2013) Tao Sang et al.   CURRENT OPINION IN PLANT BIOLOGY

Why Do More Divergent Sequences Produce Smaller Nonsynonymous/Synonymous Rate Ratios in Pairwise Sequence Comparisons?

(2013) M. dos Reis et al.   GENETICS

Hitchhiking of Deleterious Alleles and the Cost of Adaptation in Partially Selfing Species

(2013) Matthew Hartfield et al.   GENETICS

Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution

(2013) Laurent Guéguen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

(2013) Carina F. Mugal et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic signatures of selection at linked sites: unifying the disparity among species

(2013) Asher D. Cutter et al.   NATURE REVIEWS GENETICS

Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap

(2013) Philippe Gayral et al.   PLoS Genetics

The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate Ciona intestinalis

(2012) Georgia Tsagkogeorga et al.   Genome Biology and Evolution

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity

(2012) Erik C Andersen et al.   NATURE GENETICS

Parallel domestication of the Shattering1 genes in cereals

(2012) Zhongwei Lin et al.   NATURE GENETICS

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

RECOMBINATION AND HITCHHIKING OF DELETERIOUS ALLELES

(2011) Matthew Hartfield et al.   EVOLUTION

Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness

(2011) B Mangin et al.   HEREDITY

GC-Biased Gene Conversion and Selection Affect GC Content in the Oryza Genus (rice)

(2011) Aline Muyle et al.   MOLECULAR BIOLOGY AND EVOLUTION

Natural Selection in Gene-Dense Regions Shapes the Genomic Pattern of Polymorphism in Wild and Domesticated Rice

(2011) J. M. Flowers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary History of Pearl Millet (Pennisetum glaucum [L.] R. Br.) and Selection on Flowering Genes since Its Domestication

(2011) J. Clotault et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences

(2011) Zhi-Ming Li et al.   THEORETICAL AND APPLIED GENETICS

BioMart Central Portal: an open database network for the biological community

(2011) J. M. Guberman et al.   Database-The Journal of Biological Databases and Curation

Domestication Relaxed Selective Constraints on the Yak Mitochondrial Genome

(2010) Zhaofeng Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ABC as a flexible framework to estimate demography over space and time: some cons, many pros

(2010) G. BERTORELLE et al.   MOLECULAR ECOLOGY

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution

(2010) Jean-François Gout et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection

(2009) Jochen B. W. Wolf et al.   Genome Biology and Evolution

Quantitative Prediction of Molecular Clock and Ka/Ks at Short Timescales

(2009) G. I. Peterson et al.   MOLECULAR BIOLOGY AND EVOLUTION

The nature of selection during plant domestication

(2009) Michael D. Purugganan et al.   NATURE

A comparative view of the evolution of grasses under domestication

(2009) Sylvain Glémin et al.   NEW PHYTOLOGIST

Ensembl Genomes: Extending Ensembl across the taxonomic space

(2009) P. J. Kersey et al.   NUCLEIC ACIDS RESEARCH

Non-linear regression models for Approximate Bayesian Computation

(2009) Michael G. B. Blum et al.   STATISTICS AND COMPUTING

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

Detecting Local Adaptation Using the Joint Sampling of Polymorphism Data in the Parental and Derived Populations

(2008) H. Innan et al.   GENETICS

The Legacy of Domestication: Accumulation of Deleterious Mutations in the Dog Genome

(2008) F. Cruz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS